I have same problem. Playing Gigantic PerfectWorld2f map with modified size of map (282x191), 32 civs at start at game, extra civs modpack, eternity speed. Some civs were erased by Tsunami event, some emerged from barb cities. I am at middle of ancient era now, i have 7 cities, single one civ living on big separate island have 13 cities, one civ which emerged from barb civs have 2 cities, and ALL other civs have 1 city, and they are in the middle of ancient era too.
Tsunami event was erasing coastal civs, at one turn it destroyed mine, - i had to rollback some turns. So i manually turned off destroying city option for that event in XML file. This event should be either removed or redone or made optional - destroying civs (1 city ones in prehistoric) by random event is very unbalanced.
p.s. on 1st screen there is this 13 cities civ, on 2nd you can see other civs scores and cities number, on 3rd screen my settings. I also noticed that although i have Always Raze option turned off - cities were razed when captured.